I have been extracting histones using 0.8M HCl. I have used acid-soluble fraction for SDS-PAGE and subsequent WB. I found that I can actually stain extract for other nuclear proteins - for example histone-modifying enzymes (H3K4 methyltransferases, RING1B). I wonder why I can see these proteins in the extract. I doubt that they are as positively charged as histones so they are some kind of background. I am not sure how specific it is. What fraction of these proteins is extracted with this method? Could it be considered a chromatin-bound fraction specifically? Is it similar to nuclear extracts? Any thoughts from people who understand better how these extractions work?

Yes, of course, I stainded it with Coomassie. I can see a lot of protein bands on it. I just wonder if the protocol suggests that some fraction of proteins will be extracted more efficiently (like nuclear proteins or chromatin-bound proteins)?